I had this same problem with Mantano on my Transformer Infinity after upgrading it to Jelly Bean.
You don't need to do the reset every time you want to read a book in Matano, you only need to do it once.
The reason for this is that Manato's database has got corrupted by the upgrade process, it doesn't happen on all devices, just some of them. I followed the following process:
1. Cleared the app data.
2. Unistalled Mantano.
3. Deleted the Mantano folder.
4. Checked that all my data was either backed up or on my memory card, then removed the memory card.
5. Performed a factory reset via the settings menu 3 times skipping the setup until the last reset was complete. The reason for this was after reading about this on Transformerforums the Asus Transformer doesn't always clear everything on the first reset, as you don't have an Infinity, doing it 3 times may not be needed.
6. Loaded my backed up data back onto my tablet and reinstalled Mantano.
7. Set all my collections back up.
After doing this, I have not had the problem since and it has been working perfectly.
This is also the instructions Mantano give to resolve this.
So long as you are willing to do this just once, you wont get this problem again.